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using System.Collections.Generic;
using Bio.Data.Interfaces.Drawing;

namespace Bio.Data.Interfaces
{
    /// <summary>
    /// This represents an RNA secondary structure model that has base pairs, helices
    /// and loops. It can also have 2-D drawing information, labels, shapes, etc...
    /// 
    /// A secondary structure model may have an absolute rendering provided as an
    /// extensible property. If it is available, it will be used for rendering.
    /// 
    /// If a rendering is provided, the cooridinates are expected to be associated
    /// with the nucleotides
    /// </summary>
    public interface IStructureModelBioEntity
    {
        /// <summary>
        /// The underlying sequence
        /// </summary>
        IBioSequence Sequence { get; }

        /// <summary>
        /// The base pairs in the RNA secondary structure model.
        /// </summary>
        IList<IBasePairBioEntity> BasePairs { get; }

        /// <summary>
        /// The extents in the RNA secondary structure model. Currently this is loops, helices, pseudoknots.
        /// In the future, it will be extended to motifs.
        /// </summary>
        IList<IStructureExtentBioEntity> Extents { get; }
    }
}
